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Topic: Supercoiling of DNA

	Biochemistry 201: DNA Topology (Site not responding. Last check: 2007-10-21)
		Giaever, G. N., Snyder, L., and Wang, J. DNA supercoiling in vivo.
		Andersen, A. H., Svejstrup, J. and Westergaard, O. The DNA binding, cleavage, and religation reactions of eukaryotic topoisomerases I and II.
		Cozzarelli, N. DNA gyrase and the supercoiling of DNA.
	cmgm.stanford.edu /biochem201/Handouts/DNAtopo.html (484 words)

	DNA Rings: Page 2 (Site not responding. Last check: 2007-10-21)
		Negatively supercoiled DNA is a high energy state.
		Negatively supercoiled DNA is the natural form of DNA in the living cells.
		Because unwiding of DNA relieves the superhelical stress, and unwiding is a prerequisite for replication and transcription, the existence of DNA as a stressed superhelix enables to launch these processes properly.
	www.albany.edu /~achm110/dnarings2.html (159 words)

	Bi, Xin - DNA within transcriptionally silenced chromatin in Saccharamyces cerevisiae is topologically distinct from ... (Site not responding. Last check: 2007-10-21)
		This was accomplished by examining the supercoiling of DNA circles excised from the HML locus.
		These results establish that, (1) DNA in transcriptionally silenced chromatin assumes distinct topology that is not due to the lack of transcription, and (2) silencers are not required for maintaining the topology.
		We are testing the hypothesis that the higher negative supercoiling at HML is due to the fact that histones H3 and H4 in the nucleosomes at HML are hypoacetylated, which may affect the wrapping of DNA around the nucleosomal core.
	www.yeastgenome.org /yeast96/f2119.html (256 words)

	DNA SUPERCOILING AND TOPOISOMERASES (Site not responding. Last check: 2007-10-21)
		Supercoiling of DNA is an important feature of all chromosomes from those of the smallest viruses to those of eukaryotes.
		Supercoiled DNA is relaxed by nicking one strand by treatment with pancreatic DNase-1 (cleaves only one strand of DNA).
		The degree of supercoiling of bacterial DNA is thus determined by the opposing actions of two enzymes.
	education.vsnl.com /kedar (1796 words)

	Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA -- Rodríguez and Stock 21 ... (Site not responding. Last check: 2007-10-21)
		Type I topoisomerases cleave one strand of the duplex;
		The conformational changes in H2 and H3 were derived from a superposition of reverse gyrase onto the structure of PcrA helicase complexed with DNA and ADPNP (Velankar et al., 1999), and the open form of the topoisomerase gate was derived from a superposition with the putative open form of topoisomerase I (Feinberg et al., 1999).
		Lima,C.D., Wang,J.C. and Mondragón,A. (1993) Crystallization of a 67 kDa fragment of Escherichia coli DNA topoisomerase I. Mol.
	embojournal.npgjournals.com /cgi/content/full/21/3/418 (4313 words)

	Ch432_Lec_27Feb
		DNA exists as a double-stranded, anti-parallel, double helix (both strands wrap together, like a ribbon, around a common axis).
		Supercoiling allows DNA to take up a more compact form, and is a necessary consequence of replication and transcription.
		Supercoiling means that the helix is itself wrapped into a higher level coil, it is super-twisted or has super-helicity.
	www.humboldt.edu /~rap1/C432.S02/C432Notes/C432n27feb.html (917 words)

	Behavior of Supercoiled DNA -- Strick et al. 74 (4): 2016 -- Biophysical Journal
		The ~16-µm-long DNA molecule is bound to a glass surface (the bottom of a 1 mm × 1 mm × 50 mm capillary tube) at one end by digoxigenin/anti-digoxigenin links and at the other end to a superparamagnetic bead (3-µm diameter) by biotin/streptavidin links.
		Uptake of homologous single-stranded fragments by superhelical DNA.
		The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix.
	www.biophysj.org /cgi/content/full/74/4/2016 (6884 words)

	Hai-Young Wu - WSU Pharmacology
		The torsional stress placed upon DNA is integral to the regulation of gene expression, yet the mechanisms involved in these DNA supercoiling effects remain elusive.
		In our studies on the role of DNA supercoiling in the leu-500 activation phenomenon in Salmonella typhimurium topA mutants, we found a control mechanism, the promoter relay mechanism, which coordinates the expression of genes in the ilvIH-leuO-leuABCD gene cluster.
		Wu, H.-Y. and Fang, M. “ DNA supercoiling and transcription control: A model from the study of suppression of the leu-500 mutation in Salmonlla typhimurium topA- mutants.” Progress in Nucleic Acid Research and Molecular Biology, vol.
	www.med.wayne.edu /pharm/wu.htm (958 words)

	Plasmid DNA Supercoiling and Gyrase Activity in Escherichia coli Wild-Type and rpoS Stationary-Phase Cells -- ...
		DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression.
		Effect of DNA supercoiling and catabolite repression on the expression of the tetA genes in Escherichia coli.
		Conter, A. Plasmid DNA Supercoiling and Survival in Long-Term Cultures of Escherichia coli: Role of NaCl.
	jb.asm.org /cgi/content/full/185/3/1097 (2673 words)

	GAIL J. PRUSS (Site not responding. Last check: 2007-10-21)
		Supercoiling is a structural feature of topologically constrained DNA molecules, such as circular chromosomes and linear chromosomes whose ends are not free to rotate.
		Supercoiling greatly affects the substrate properties of DNA and has been shown to be important in replication, transcription, recombination, repair, and transposition in bacteria.
		Her studies on the effects of topoisomerase mutations on plasmid DNA supercoiling have revealed dramatic sequence- dependent changes that are due to transcription, indicating that transcription is an important determinant of supercoiling in bacteria.
	www.biol.sc.edu /faculty/pruss.html (293 words)

	DNA Supercoiling Factor Localizes to Puffs on Polytene Chromosomes in Drosophila melanogaster -- Kobayashi et al. 18 ...
		DNA supercoiling factor (SCF) was first identified in silkworm as a protein that generates negative supercoils in DNA in conjunction
		Supercoiled DNA with 10 or more negative superhelical turns migrated faster than linear DNA in the first dimension (19).
		Purification of a DNA supercoiling factor from the posterior silk gland of Bombyx mori.
	mcb.asm.org /cgi/content/full/18/11/6737 (4584 words)

	Topoisomerase IV, alone, unknots DNA in E. coli -- Deibler et al. 15 (6): 748 -- Genes and Development
		Int-mediated DNA knots and the catenated intermediates of DNA replication are toroidal, right-handed, and positive in structure.
		Pollock, T.J. and Nash, H.A. Knotting of DNA caused by a genetic rearrangement.
		Rodriguez-Campos, A. DNA knotting abolishes in vitro chromatin assembly.
	www.genesdev.org /cgi/content/full/15/6/748 (7397 words)

	Failure to Relax Negative Supercoiling of DNA Is a Primary Cause of Mitotic Hyper-recombination in ...
		Failure to Relax Negative Supercoiling of DNA Is a Primary Cause of Mitotic Hyper-recombination in Topoisomerase-deficient Yeast Cells -- Trigueros and Roca 277 (40): 37207 -- Journal of Biological Chemistry
		DNA Extraction and Electrophoretic Analysis-- DNA from transformed yeast cells was prepared from yeast spheroplast (24).
		DNA from the strain JCW28 transformed with the Yp 3.4 minicircle and either harboring a control plasmid (lanes 1, 3, and 5) or expressing the S.
	www.jbc.org /cgi/content/full/277/40/37207 (2943 words)

	Monte Carlo Implementation of Supercoiled Double-Stranded DNA -- Yang et al. 78 (4): 1979 -- Biophysical Journal
		is insensitive to the supercoiling degree of the polymer; and
		The current conformation of the DNA central axis is shown by solid lines and the trial conformation by dashed lines.
		In conclusion, the elasticity of supercoiled double-stranded DNA is investigated by Monte Carlo simulations.
	www.biophysj.org /cgi/content/full/78/4/1979 (4192 words)

	DNA Supercoiling (Site not responding. Last check: 2007-10-21)
		L is invariant for a given DNA molecule as long as the covalent structure remains intact.
		In any double stranded closed circular DNA (ie a molecule with a fixed linking number), a balance will be achieved where the energy of distorting the local helical conformation of the molecule (T) is offset by the energy required to constrain the 3-dimensional path (W) of the molecule.
		The resulting negative supercoils favor reactions which would lead to unwinding of the double helix, such as the action of polymerases which need a single stranded template for activity.
	www.olemiss.edu /courses/chem471/NA/DNAsupercoil.html (369 words)

	DNA supercoiling (Site not responding. Last check: 2007-10-21)
		The role of gene expression herein was conceived of as in terms of a dictatorial hierarchy, neglecting the possibility of a feedback from the level of the three energy potentials to transcription of the genes.
		Prokaryotic DNA is supercoiled by the action of DNA gyrase under concomitant hydrolysis of ATP.
		Westerhoff and colleagues have demonstrated that in vitro the extent of DNA supercoiling achieved by DNA gyrase is strongly sensitive to the magnitude of DGp [Westerhoff et al., 1988].
	www.bio.vu.nl /vakgroepen/microb/main/superc.html (471 words)

	Cell-Free Transcription at 95{degrees}: Thermostability of Transcriptional Components and DNA Topology Requirements of ...
		DNA was subsequently analyzed by electrophoresis on 10% agarose gels and stained with ethidium bromide.
		DNA topoisomerase I in the presence of ethidium bromide.
		Plasmid pLUW479 in different conformations, negatively supercoiled (--), slightly negatively supercoiled (-), relaxed (o), slightly positively supercoiled (+), and positively supercoiled (++) was used as template in cell-free transcription reactions, and the RNA was analyzed by primer extension.
	www.genetics.org /cgi/content/full/152/4/1325 (4623 words)

	DNA Topoisomerase (Site not responding. Last check: 2007-10-21)
		DNA Topoisomerase: DNA Topoisomerase is an enzyme that alters the supercoiling of double-stranded DNA.
		DNA Topoisomerase acts by transiently cutting one or both strands of the DNA.
		DNA Topoisomerase type I cuts one strand whereas DNA topoisomerase type II cuts both strands of the DNA.
	www.horizonpress.com /gateway/dna-topoisomerase.html (147 words)

	Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study
		Duplex DNA is represented as a chain of hydrodynamic beads interacting through potentials of linearly elastic stretching, bending, and twisting, as well as excluded volume.
		Following a sharp rise at early times, the distributed twist assumes a nearly constant value in both subdomains, and a succession of supercoiling deformations occurs as superhelical stress is increasingly partitioned to writhe.
		U.S.A. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA.
	repositories.cdlib.org /postprints/270 (307 words)

	Chemistry :: Effect of Varying the Supercoiling of DNA on Transcription and Its Regulation :: Pharmaceutical ... (Site not responding. Last check: 2007-10-21)
		Transcription of many genes, like other DNA transactions, is affected by DNA supercoiling.
		Negative supercoiling of the DNA template is usually more efficient for transcription.
		(ii) DNA is underwound in open and elongating complexes, and underwinding is favored by negative supercoiling.
	www.pharmainfo.net /displayarticle5865.html (226 words)

	Visualization of unconstrained negative supercoils of DNA on polytene chromosomes of Drosophila -- Matsumoto and Hirose ...
		Detection of negative supercoils of DNA on hsp70 in salivary gland.
		Genomic DNA was digested with BglII and EcoRI, and analyzed as in (B) using DDS fragment as a probe.
		Effect of previous nicking of DNA or inhibition of transcription on psoralen signals on heat-shock puffs.
	jcs.biologists.org /cgi/content/full/117/17/3797 (4299 words)

	DNA SUPERCOILING UNDER HIGH PRESSURE (Site not responding. Last check: 2007-10-21)
		In this presentation, DNA supercoiling under high pressure has been studied in vitro by the use of two methods: relaxation of supercoiled closed-circular plasmid DNA by wheat germ topoisomerase I, and re-cyclization of linear plasmid DNA by T4 DNA ligase.
		Results The relaxation reaction of plasmid pBR322 DNA was found to be sensitive for pressure elevations, while the effect of pressure on the structure-activity relationship of topoisomerase I was either insufficient or reversible.
		The observations that DNA adopts higher superhelicity under high pressure suggest an involvement of volume changes in the transitions in DNA topological conformations.
	www.rzuser.uni-heidelberg.de /~u53/poster-abstracts/kunugi1.html (355 words)

	PHRI :: Karl Drlica, Ph.D.
		Mutation in the DNA gyrase A Gene of Escherichia coli that expands the quinolone resistance-determining region.
		Heddle JG, Lu T, Zhao X, Drlica K, Maxwell A. gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity.
		In DNA Cleavers and Chemotherapy of Cancer or Viral Diseases, edited by B. Meunier, Kluwer Academic Publishers, Dordrecht, pp 91-106.
	www.phri.org /research/res_pidrlica.asp (1509 words)

	Protein A gene expression is regulated by DNA supercoiling which is modified by the ArlS-ArlR two-component system of ... (Site not responding. Last check: 2007-10-21)
		Protein A gene expression is regulated by DNA supercoiling which is modified by the ArlS-ArlR two-component system of Staphylococcus aureus -- Fournier and Klier 150 (11): 3807 -- Microbiology
		Protein A gene expression is regulated by DNA supercoiling which is modified by the ArlS–ArlR two-component system of Staphylococcus aureus
		DNA supercoiling modulators on spa expression, suggesting that
	mic.sgmjournals.org /cgi/content/abstract/150/11/3807 (262 words)

	Profile
		Our lab's goals are to elucidate how recombination and DNA break repair are accomplished and how they are regulated to occur at the proper place and time.
		We are testing the hypothesis that the observed pause of DNA unwinding at Chi reflects the cessation of the RecD helicase at Chi and the continued movement of the RecB ss DNA translocase along the loop up to Chi.
		Taylor A, Smith GR,Unwinding and rewinding of DNA by the RecBC enzyme.
	myprofile.cos.com /smithabc102 (2891 words)

	Topoisomerase (Site not responding. Last check: 2007-10-21)
		Topoisomerase: Topoisomerase is an enzyme that alters the supercoiling of double-stranded DNA.
		Topoisomerase type I cuts one strand whereas topoisomerase type II cuts both strands of the DNA.
		Topoisomerase relaxes the coil and extends the DNA molecule.
	www.horizonpress.com /gateway/topoisomerase.html (128 words)

	Active-Site Residues of Escherichia coli DNA Gyrase Required in Coupling ATP Hydrolysis to DNA Supercoiling and Amino ...
		Active-Site Residues of Escherichia coli DNA Gyrase Required in Coupling ATP Hydrolysis to DNA Supercoiling and Amino Acid Substitutions Leading to Novobiocin Resistance -- Gross et al.
		Active-Site Residues of Escherichia coli DNA Gyrase Required in Coupling ATP Hydrolysis to DNA Supercoiling and Amino Acid Substitutions Leading to Novobiocin Resistance
		DNA gyrase is a bacterial type II topoisomerase which couples
	aac.asm.org /cgi/content/abstract/47/3/1037 (407 words)

	Shiladitya DasSarma
		Current efforts are directed at computational and functional genomics of NRC-1 using a battery of approaches, including DNA arrays, proteomics, and reverse genetics.
		Another on-going project in the lab is directed at deciphering the regulation of genes coding for the photosynthetic purple membrane in halobacteria, expression of which is modulated by oxygen and light.
		Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker.
	www.umbi.umd.edu /~comb/faculty/dassarma/dassarma.html (656 words)

	DNA Supercoiling (Site not responding. Last check: 2007-10-21)
		TXn is initiated more efficiently when DNA is supercoiled
		The efficency of some promoters is influenced by degree of supercoiling
		Txn has a significant effect on the local DNA structure
	classweb.gmu.edu /achriste/COP_000A-html.PPT/sld040.htm (30 words)

	DNA Supercoiling Factor Localizes to Puffs on Polytene Chromosomes in Drosophila melanogaster -- Kobayashi et al. 18 ... (Site not responding. Last check: 2007-10-21)
		Received 14 May 1998/Returned for modification 14 July 1998/Accepted 14 August 1998
		Hossain, M. S, Kurokawa, K., Akimitsu, N., Sekimizu, K. DNA topoisomerase II is required for the G0-to-S phase transition in Drosophila Schneider cells, but not in yeast.
		Yang, X., Li, W., Prescott, E. D., Burden, S. J., Wang, J. DNA Topoisomerase II and Neural Development.
	mcb.asm.org /cgi/content/abstract/18/11/6737 (365 words)

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